Team:NRP-UEA-Norwich/Modeling/3D

3D Modelling Overview

We built 3D models to see how changing parameters such as branching degree and the number of tiers affect the overall structure of the molecule in a chemically accurate way.

Glycogen

Glycogen is the glucose storage molecule in animals, bacteria and fungi. It is a polysaccharide composed of monosaccharide glucose units linked by alpha-1,4 glycosidic bonds. Each linear chain contains approximately 13 glucose residues and a number of alpha-1,6 glycosidic bonds, which allow branching, that are 3–4 residues apart. Glycogen is the analogue of starch in plants but is more extensively branched and compact.

This simple model - created for our wiki by the SWEET software - shows a small section of a glycogen molecule consisting of 91 glucose units which are contained within 7 branches and 3 tiers. The 1,4 linked sections can be seen to coil into a helical shape, and the 1,6 linkages form helical branches away from the centre of the molecule.

You can interact with the model using your mouse.

3D Printing

We developed a pipeline to 3D print these molecules. After several attempts, we managed to have our own 3D printed molecule!

The process of creating a 3D model that is valid to be 3D printed from a PDB file, which is a textual file format describing the three-dimensional structures of molecules, turned out to be very challenging. After what seemed like an impossible task and a number of failed attempts, we managed to successful create a valid 3D model that could be printed. The print itself took just over 28 hours.

3D Printing Gallery

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References

http://www.biotopics.co.uk/jsmol/glycogen.html

http://watcut.uwaterloo.ca/webnotes/Metabolism/glycogenStructure.html.

http://www.glycosciences.de/modeling/sweet2/doc/index.php